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(-) Description

Title :  PANTOTHENATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS (MTPANK) IN COMPLEX WITH AMPPCP AND PANTOTHENATE
 
Authors :  B. Chetnani, S. Das, P. Kumar, A. Surolia, M. Vijayan
Date :  05 Sep 08  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Homodimer, Coa Biosynthesis, Nucleotide Binding, Atp- Binding, Coenzyme A Biosynthesis, Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Chetnani, S. Das, P. Kumar, A. Surolia, M. Vijayan
Mycobacterium Tuberculosis Pantothenate Kinase: Possible Changes In Location Of Ligands During Enzyme Action
Acta Crystallogr. , Sect. D V. 65 312 2009
PubMed-ID: 19307712  |  Reference-DOI: 10.1107/S0907444909002170

(-) Compounds

Molecule 1 - PANTOTHENATE KINASE
    Chains: A
    EC Number: 2.7.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28A(+) (NOVAGEN)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: COAA (RV1092C)
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: MTPANK, PANTOTHENIC ACID KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 17)

Asymmetric Unit (6, 17)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2EDO6Ligand/Ion1,2-ETHANEDIOL
3FLC1Ligand/IonCITRATE ANION
4GOL6Ligand/IonGLYCEROL
5NA2Ligand/IonSODIUM ION
6PAU1Ligand/IonPANTOTHENOIC ACID
Biological Unit 1 (5, 30)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2EDO12Ligand/Ion1,2-ETHANEDIOL
3FLC2Ligand/IonCITRATE ANION
4GOL12Ligand/IonGLYCEROL
5NA-1Ligand/IonSODIUM ION
6PAU2Ligand/IonPANTOTHENOIC ACID

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:39 , GLU A:42 , VAL A:99 , ALA A:100 , VAL A:101 , GLY A:102 , LYS A:103 , SER A:104 , THR A:105 , ARG A:108 , HIS A:179 , ARG A:238 , MET A:242 , HOH A:447 , PAU A:600 , EDO A:904BINDING SITE FOR RESIDUE ACP A 500
02AC2SOFTWARETYR A:235 , ARG A:238 , PHE A:239 , MET A:242 , ILE A:272 , ACP A:500 , EDO A:901BINDING SITE FOR RESIDUE PAU A 600
03AC3SOFTWAREALA A:66 , ARG A:69 , ALA A:73 , GLU A:76BINDING SITE FOR RESIDUE GOL A 800
04AC4SOFTWARELEU A:286 , ARG A:289 , PRO A:290 , ARG A:308BINDING SITE FOR RESIDUE GOL A 801
05AC5SOFTWAREARG A:146 , GLU A:283BINDING SITE FOR RESIDUE GOL A 802
06AC6SOFTWAREASP A:183 , ILE A:184 , LEU A:240 , ALA A:241 , ARG A:243 , THR A:244BINDING SITE FOR RESIDUE GOL A 803
07AC7SOFTWARETYR A:177 , SER A:178 , HIS A:179 , LEU A:180 , EDO A:905BINDING SITE FOR RESIDUE GOL A 806
08AC8SOFTWAREARG A:15 , GLN A:43 , ASP A:45 , GLU A:48 , SER A:303BINDING SITE FOR RESIDUE EDO A 900
09AC9SOFTWARELYS A:147 , TYR A:182 , PAU A:600BINDING SITE FOR RESIDUE EDO A 901
10BC1SOFTWARELEU A:125 , VAL A:126 , THR A:127 , GLN A:190BINDING SITE FOR RESIDUE EDO A 902
11BC2SOFTWARESER A:263 , VAL A:267 , ARG A:270BINDING SITE FOR RESIDUE EDO A 903
12BC3SOFTWAREARG A:38 , ARG A:108 , ARG A:140 , HOH A:447 , ACP A:500BINDING SITE FOR RESIDUE EDO A 904
13BC4SOFTWAREASP A:129 , GLY A:130 , TYR A:177 , HIS A:179 , HOH A:448 , GOL A:806BINDING SITE FOR RESIDUE EDO A 905
14BC5SOFTWAREARG A:122 , ARG A:193 , HIS A:194BINDING SITE FOR RESIDUE FLC A 650
15BC6SOFTWAREARG A:122 , ASP A:124 , ARG A:193BINDING SITE FOR RESIDUE NA A 950
16BC7SOFTWARELYS A:166 , LEU A:312BINDING SITE FOR RESIDUE NA A 951

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZSE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZSE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZSE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZSE)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZSE)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:307
 aligned with COAA_MYCTO | P9WPA6 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:307
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       
           COAA_MYCTO     6 EPSPYVEFDRRQWRALRMSTPLALTEEELVGLRGLGEQIDLLEVEEVYLPLARLIHLQVAARQRLFAATAEFLGEPQQNPDRPVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTDGFLYPNAELQRRNLMHRKGFPESYNRRALMRFVTSVKSGSDYACAPVYSHLHYDIIPGAEQVVRHPDILILEGLNVLQTGPTLMVSDLFDFSLYVDARIEDIEQWYVSRFLAMRTTAFADPESHFHHYAAFSDSQAVVAAREIWRTINRPNLVENILPTRPRATLVLRKDADHSINRLRLRKL 312
               SCOP domains d2zsea_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2zseA00 A:6-312 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhh........hhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeee....hhhhhhhhhhhhhhh......eeeee.hhhh.hhhhhhhh.......hhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeeeee....eeeeee..........hhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zse A   6 EPSPYVEFDRRQWRALRMSTPLALTEEELVGLRGLGEQIDLLEVEEVYLPLARLIHLQVAARQRLFAATAEFLGEPQQNPDRPVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTDGFLYPNAELQRRNLMHRKGFPESYNRRALMRFVTSVKSGSDYACAPVYSHLHYDIIPGAEQVVRHPDILILEGLNVLQTGPTLMVSDLFDFSLYVDARIEDIEQWYVSRFLAMRTTAFADPESHFHHYAAFSDSQAVVAAREIWRTINRPNLVENILPTRPRATLVLRKDADHSINRLRLRKL 312
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       


Chain A from PDB  Type:PROTEIN  Length:307
 aligned with COAA_MYCTU | P9WPA7 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:307
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       
           COAA_MYCTU     6 EPSPYVEFDRRQWRALRMSTPLALTEEELVGLRGLGEQIDLLEVEEVYLPLARLIHLQVAARQRLFAATAEFLGEPQQNPDRPVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTDGFLYPNAELQRRNLMHRKGFPESYNRRALMRFVTSVKSGSDYACAPVYSHLHYDIIPGAEQVVRHPDILILEGLNVLQTGPTLMVSDLFDFSLYVDARIEDIEQWYVSRFLAMRTTAFADPESHFHHYAAFSDSQAVVAAREIWRTINRPNLVENILPTRPRATLVLRKDADHSINRLRLRKL 312
               SCOP domains d2zsea_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2zseA00 A:6-312 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhh........hhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeee....hhhhhhhhhhhhhhh......eeeee.hhhh.hhhhhhhh.......hhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeeeee....eeeeee..........hhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zse A   6 EPSPYVEFDRRQWRALRMSTPLALTEEELVGLRGLGEQIDLLEVEEVYLPLARLIHLQVAARQRLFAATAEFLGEPQQNPDRPVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTDGFLYPNAELQRRNLMHRKGFPESYNRRALMRFVTSVKSGSDYACAPVYSHLHYDIIPGAEQVVRHPDILILEGLNVLQTGPTLMVSDLFDFSLYVDARIEDIEQWYVSRFLAMRTTAFADPESHFHHYAAFSDSQAVVAAREIWRTINRPNLVENILPTRPRATLVLRKDADHSINRLRLRKL 312
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ZSE)

(-) Gene Ontology  (16, 25)

Asymmetric Unit(hide GO term definitions)
Chain A   (COAA_MYCTU | P9WPA7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004594    pantothenate kinase activity    Catalysis of the reaction: ATP + pantothenate = ADP + D-4'-phosphopantothenate.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004849    uridine kinase activity    Catalysis of the reaction: ATP + uridine = ADP + UMP.
biological process
    GO:0015937    coenzyme A biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006206    pyrimidine nucleobase metabolic process    The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
    GO:0043097    pyrimidine nucleoside salvage    Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A   (COAA_MYCTO | P9WPA6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004594    pantothenate kinase activity    Catalysis of the reaction: ATP + pantothenate = ADP + D-4'-phosphopantothenate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0015937    coenzyme A biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        COAA_MYCTO | P9WPA6: 2ges 2get 2geu 2gev 2zs7 2zs8 2zs9 2zsa 2zsb 2zsd 2zsf 3aez 3af0 3af1 3af2 3af3 3af4 3avo 3avp 3avq 4bfs 4bft 4bfu 4bfv 4bfw 4bfx 4bfy 4bfz
        COAA_MYCTU | P9WPA7: 2ges 2get 2geu 2gev 2zs7 2zs8 2zs9 2zsa 2zsb 2zsd 2zsf 3aez 3af0 3af1 3af2 3af3 3af4 3avo 3avp 3avq 4bfs 4bft 4bfu 4bfv 4bfw 4bfx 4bfy 4bfz

(-) Related Entries Specified in the PDB File

2ges PANTOTHENATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS (MTPANK) IN COMPLEX WITH A COENZYME A DERIVATIVE, FORM-I (RT)
2get PANTOTHENATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS (MTPANK) IN COMPLEX WITH A COENZYME A DERIVATIVE, FORM-I (LT)
2geu PANTOTHENATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS (MTPANK) IN COMPLEX WITH A COENZYME A DERIVATIVE, FORM-II (RT)
2gev PANTOTHENATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS (MTPANK) IN COMPLEX WITH A COENZYME A DERIVATIVE, FORM-II (LT)